


Understand Me

by WaywardFairchild



Series: Free Me Series [4]
Category: Marvel Cinematic Universe, Spider-Man (Tom Holland Movies), Spider-Man - All Media Types
Genre: Alternate Origin Story, Hurt Peter Parker, Hurt Tony Stark, Multi, Pepper Potts Acting as Peter Parker's Parental Figure, Peter Parker & Morgan Stark are Siblings (Marvel Cinematic Universe), Peter Parker Needs a Hug, Peter Parker is Tony Stark's Biological Child, Protective Harley Keener, Protective Harry Osborn, Tony Stark Needs a Hug, Uncle James "Rhodey" Rhodes
Language: English
Status: Completed
Published: 2020-09-13
Updated: 2020-10-11
Packaged: 2021-03-06 17:14:32
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 5
Words: 10,016
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/26442526
Author URL: https://archiveofourown.org/users/WaywardFairchild/pseuds/WaywardFairchild
Summary: Peter Stark has gone MIA again. Tony must find his son and figure out what is going on while a new threat is coming on the horizon and will change Peter's life forever.
Relationships: Harley Keener/Peter Parker/Harry Osborn
Series: Free Me Series [4]
Series URL: https://archiveofourown.org/series/1768429
Kudos: 25





	1. Peter Parker or Peter Stark

Present Day, New York

Harley and Harry had not heard from their Peter. Harry had tried the other boy’s phone while Harley had FRIDAY search for Peter. They knew that Peter wouldn’t leave. They were worried that someone had kidnapped Peter again. Tony hadn’t realized his son being missing until Harley and Harry said something. Peter had been to himself before he completely disappeared. Tony tried his phone but Peter seemed to be ignoring him. Tony knew he had to find his son. He was worried that something happened and Peter ran away without Harley and Harry again. 

“Maybe we should have FRIDAY track him,” Harley said. Harley and Harry were overly worried about Peter. Peter wouldn’t have disappeared unless something happened. They didn’t know if they did something wrong. They were worried about what they were going to do or how they would find him. Harley ended up getting Peter’s location when FRIDAY found a photo of Peter in Malibu. By the time FRIDAY found Peter, it had been a week of them searching for the boy. Tony looked at his boy in the photo. Peter looked stressed as if something was there that Tony wasn’t supposed to know. He was hiding behind a baseball cap and had on a hoodie but Tony saw his son’s worried face as he walked down the street. 

“When was this?” Tony asked FRIDAY.

“This was ten minutes ago,” FRIDAY told him. Tony knew where he had to go. He looked at the other two boys. 

“I got to go get him this time. I think I know where he might go if he needs to think,” Tony said. The other two went to protest but Tony gave them a look. He knew he couldn’t stop them but he would need to this time.

“Peter isn’t ready to talk to us about whatever is wrong but I need to talk to him alone to see what it is and see if we can help him,” Tony told them. The two boys finally agreed but only if Tony let them know as soon as possible what was going on and how they could help. Tony had been worried about this relationship but seeing that his son’s boyfriends would protect him no matter the situation he felt confident about the relationship. 

Pepper stopped Tony before he left. She had been worried about her son. Peter was now found and she needed to know. 

“Any word?” She asked.

“His in Malibu. I’m heading there now. Can you send a Quinjet behind me to take us home?” Tony asked. Pepper agreed as she told Tony to be safe as he got into the suit before he flew off to find his son. 

~

Present Day, Malibu, CA

Peter had been to see his mother’s grave. He spent every day at her grave yelling at her. He blamed her for not being there even though he knew she died having him. He shouldn’t blame her but he needed to blame someone. She had to know who his birth father was. She could have stopped all of this. He figured Richard must have known. Peter went to the old Malibu mansion that was in ruins after a week of yelling at his mother. He was watching the waves that he grew up seeing. He remembered when he got the news of the mansion being destroyed. He had been away and when he heard he was upset. He had grown up here in this home. His first memories were in the mansion.

“You know I was thinking about having it rebuilt,” a voice said. Peter turned to see his father. He knew he had been gone for a week but he figured Tony wouldn’t have noticed.

“I guess running away was a stupid idea,” Peter joked. Tony didn’t find it funny. 

“What is bothering you this time, Bambi?” Tony asked his son. 

“I just wanted to see Mom,” Peter said. Tony looked at him confused. Pepper was back in New York with Morgan. 

“Your mom misses you,” Tony said.

“Pepper maybe took on the role of my mom but she isn’t my birth mom and I will never get to know her because I’m the reason she is dead,” Peter said. There were tears in his eyes. 

“Whatever happened to your birth mother wasn’t your fault,” Tony said wishing now he knew what happened to his kid’s birth mother. He had heard the bare minimum from Pepper about Richard being the reason why she died but by Peter’s expression, there was more to the story. 

“Do you know the name Mary Fitzpatrick?” Peter asked. Tony did. Tony remembered her. A Personal Assistant to his that quit when they broke up. It was kept quiet that they dated but she had left him.

“She was a PA for me,” Tony said.

“That you slept with,” Peter said. Tony heard his voice change when he said that. He was blaming Tony for something. 

“I dated her as well,” Tony said. “I thought I was in love with her before she left me. Not long after, Pepper started for me.”

~

_ January 2000, Malibu, California _

_ Tony Stark hated his newest assistant. She was following all the rules and staying clear of him. He had a thing for her already but he had a feeling that Obadiah would fire her if he knew they were sleeping together. That happened to the last one. _

_ “Mary,” Tony said as she entered his workshop annoyed.  _

_ “I told you I need these papers signed before you left the office yesterday,” She said annoyed with the Tony Stark. The man was surprised that she would speak to him like that. His last PA was scared to even look at him funny, but not Mary.  _

_ “You know if you were just a little nicer then maybe we could work better together,” Tony said.  _

_ “I’m not some slut to get into bed,” Mary told him. _

_ “I don’t want you in bed. I just want you to be a little nicer. It looked better on the company,” Tony said. Mary rolled her eyes but handed him the papers which he signed. Before she left she gave him one more look. _

_ “If you did want to pursue something before we got into bed my statement might change,” She said before she disappeared. It would take Tony a couple months before the two of them got together and even after that it was a while before they were together in any other way. The relationship ended when Mary left him. She didn’t want to be seen sleeping with her boss. Tony agreed. Mary had figured New York would treat her better. She didn’t think about what would happen when she meets a man who would end up being her death.  _

~

Present Day, Malibu, CA

Peter stood up annoyed with his father. He had just seemed to ignore the situation. Maybe he didn’t have everything, but Peter was angry and his mother wasn’t here to blame.

“Mary Fitzpatrick was Pepper’s half-sister. I’m Mary’s son,” Peter said. Tony was confused. Tony had known that Pepper had a half-sister who was Peter’s mother but he didn’t think it was Mary. He also didn’t see why it was important that Peter told him this. 

“Bambi, what are you trying to tell me?” Tony asked his son. Peter tried to find the right words but his anger wasn’t helping so he pulled out the paternity test and handed it to Tony. Tony looked at the first one. Tony saw how it was running against Peter and Richard. When he saw the result, he was surprised. He didn’t think it was possible that Peter could be anyone else’s son. He looked at the second paper and froze. The test was against his and Peter’s DNA. He looked at everything and it was like getting news that he already knew. Peter was biological his son. No one could claim otherwise. 

“How long have you known?” Tony asked.

“A week. Harry said something that made me think about my time in captivity and something just didn’t add up so I ran both tests,” Peter said. Tony pulled his son closer as Peter cried into his shoulder.

“It’s okay. This doesn’t change anything. It just proves something we already know. Even if it went the other way it wouldn’t change anything,” Tony told his son as Peter continued to cry while Tony made sure Peter knew he was safe. Peter cried as he held on to his father. 

“Dad, can we go home?” Peter asked. Tony nodded as they finally got up and helped his son up.

“How did you get out here?” Tony asked. 

“Uber,” Peter said. Tony heard the jets as the two looked up to see the Quinjet landing. Peter looked at his father. 

“I had your mom send a Quinjet behind me,” Tony said. “Let’s go home.” Peter nodded as the two got on the Quinjet. Peter cuddled up to Tony as his father looked at Happy who seemed annoyed at the younger boy. Peter didn’t notice the glare as they headed home. 

~

_ September 2004, Malibu, CA _

_ “Daddy,” Peter called out to his dad as he ran up behind Tony and hide behind him. Tony was confused by the boy. Pepper came out looking at Tony.  _

_ “I need to get Peter so he can have a bath,” Peter said. Peter shook his head. Tony seemed surprised that the boy was coming to him for protection. He had never really been there for the boy.  _

_ “I haven’t seen him,” Tony said as Peter seemed to sigh.  _

_ “You haven’t? Well, I guess I will have to find him and he won’t be getting an evening treat,” Pepper said.  _

_ “Well more for me then,” Tony said. Peter moved from behind Tony as he ran over to Pepper. _

_ “I know I shouldn’t have run,” Peter said. Peter looked at Pepper with pleading eyes.  _

_ “No, you shouldn’t have,” Pepper said. “Now let’s go get you bathed.” Peter nodded but look at his dad. _

_ “Daddy, can we play after my bath?” Peter said Tony looked at his list of jobs before looking back at his son.  _

_ “Maybe if I have time,” Tony told the boy before Pepper picked him up and cared him away. Tony watched his son leave as Peter watched him. Tony almost felt bad for Peter. The boy was just wanting to spend time with Tony, but Tony didn’t want his son to get attached. Peter was just here to be the heir of his company. Someone was expecting him to make a mistake and Peter was supposed to be that supposed mistake.  _

~

Present Day, New York

Harley and Harry were waiting for the call. It had been ten hours before Tony called. Harley and Harry looked at Pepper when they answered. 

“He is asleep and we should be there in about a few hours,” Tony told them. 

“Is he okay?” Pepper asked.

“Just going through something. We will talk when I get home. Just know Peter is alright and that he is only mad at me,” Tony said. Pepper seemed confused but she let Tony make sure her son was safe. 

“Are you both on your way back?” Pepper asked.

“We are Mom,” Peter’s voice said. Pepper seemed to smiled in relief.

“Peter,” Harley and Harry said.

“Sorry I worried you guys,” Peter said. “I just needed some time to think about some stuff.” 

“It’s okay,” Harley said.

“We are just glad to know you are alright,” Harry said. Peter seemed to go quiet as Tony muttered something to the boy.

“We should be home in a few hours,” Tony said. Pepper and the two boys let Tony know they understand. As so as the call ended, Tony texted them that Peter was dealing with something that they would need to comfort. Pepper didn’t understand what was happening but she had to figure it out. When the boys went to watch a movie, she went into the system and asked FRIDAY to look at anything with Peter. She didn’t say anything to the boys figuring that they would be curious but she needed to know why Peter was upset.


	2. Goblin

**Summary for the Chapter:**

> Norman is up to something, the Goblin attacks Stark Tower, Peter makes a life-changing decision

Norman Osborn was handed a few files. He was irritated when the files came in. The investigator left him with information that made him want to hurt someone. Luckily, he could just hunt down Stark and take his revenge. One file in particular made him mad. He had figured that letting his son marry the young Stark would give him the keys to the kingdom, but instead, Peter led to nothing in particular. The boy wasn’t even Tony’s son. Just a disgraced child who had nothing in this life. He would never have anything and that was what irked the man. His son would have to pay for everything the boy wanted. 

“I guess I have to take care of the matter myself,” Norman said. He threw down the files as he went to a room beside his office and injected a green liquid into his veins before he got into a suit. He would get his revenge on the Starks. Harry would be safe away from them. He went out knowing he would get his revenge on the Stark family.

~

Goblin had been an issue for a week before he attacked Stark Tower. It just happened to be the week that Peter was missing so most of the Avengers were preoccupied. A few had run-ins with the new villain but nothing serious came of the run-ins so the Avengers focused on finding the missing billionaire child. Again. 

Goblin hadn’t been a problem until he attacked Stark Tower. Harry and Harley helped get Morgan to safety as Pepper tried to get a hold of Tony and Peter. She knew that they would be landing anytime now and that they would be in danger. She called Rhodey so he could be ready to help both of them in once they got to the tower. The rest of the Avengers were on route to help with Rhodey dealing with the Goblin when the plane started to land. Pepper watched as Rhodey dealt with the Goblin as Tony saw what was going on. Tony and Peter rushed to get inside before they were spotted. Pepper watched as the Goblin went after them. Tony called a suit so he could fight them. Before she knew it her husband was in the fight but his son made it in the building. She sighed too soon though. The next thing she saw was Tony’s suit malfunction as Rhodey rushed to get to the other man. The Goblin disappeared as if he accomplished his goals. 

~

Peter and Tony landed with no problems. It was once they landed that Tony saw the issue. Rhodey was facing a goblin-like creature who was attacking his tower. Peter looked at his dad wondering what they should do. 

“I’m going to get you inside and once you are there I’ll help Rhodey,” Tony told Peter. Peter nodded before the two hurried for the entrance into the tower. They were almost there when Peter sensed the goblin and warned his father. 

“Get inside,” Tony said as he called a suit. Peter did as he was told. He knew not to go against his father’s wishes. He was safe when he saw the Goblin hit his father’s suit with something as the suit powered off and his father crashed into the tower. The Goblin left as Rhodey got his father and carried him in. Peter followed Rhodey until they reached MedBay where some guards stopped him. 

“I need to make sure he is okay,” Peter said.

“Doctor Cho will allow no one in at this time,” The men said.

“Do you even know who I am?!” Peter asked. 

“Sir you need to calm down,” the men said.

“I am the son of Tony Stark. You can’t treat me as if I’m less because I am his son and he is my father,” Peter said. Harry and Harley appeared as he continued to rant to the guards. Both boys seemed confused. 

“Peter, you are confusing them,” Harley said. “They don’t understand Italian.” The realization hit Peter’s brain. He had been speaking Italian with his dad the whole trip home. Of course, he forgot the guards don’t speak it. He must have seemed crazy. He probably didn’t realize he was speaking another language but they had. 

“Papa and I were speaking Italian on the ride home. I must have been worked up and went back to it,” Peter admitted. 

“Your dad is going to be okay,” Harley said. Peter started to cry as Harley pulled him into a hug. Harry held on to the boy as well. The three held on to each other as Pepper came down confused by what was going on. 

“Has Helen said anything?” she asked the men.

“Nothing yet,” they said. Pepper nodded as Harley and Harry moved away so Pepper could check her son for any injuries.

“I was so worried,” she said. 

“I’m fine now,” Peter said, looking down feeling ashamed at running from home for the first time since he got home. Pepper pulled him into a hug. 

“I know you may not be ready to talk about it yet but please know that I am here for you and that I will be here no matter what happens,” Pepper said.

“Of course Mom,” Peter said, feeling the tears that were still there from the day. He was wanting to just lay in bed and hide or cuddle up to his father but he knew he had to face whatever happened. 

~

Cho came out after a while to give them a report. He had broken a few bones but she was more worried that he hadn’t woken up yet. Peter looked worried as he was allowed to see his father. Peter never liked it when they were at the hospital. He never knew why. Maybe it was some unconscious before he was born memory that haunted him. Or it could just be that he didn’t like the feeling of being there. 

“Hey Dad,” Peter said, sitting by him knowing that Tony should still be able to hear him. “I should have helped you out. I should have been able to stop you from getting hurt. All of this is my fault. I should have just told you where I wanted to go so we could have seen her together. I was the reason Mom died and now I am the reason you are hurt.”

Pepper came in so Peter stopped. She would try to say it wasn’t his fault. That Tony would have never let him fight but Tony was now in a coma. Peter looked at his father and just knew what he had to do. His dad would murder him if he found out but he had to take down the Goblin once and for all. That would be his present to his father.

~

Harry went to check on his father. He knew it was only right after leaving the man alone for so long. Norman hadn’t noticed his son’s absence again though he wouldn’t notice if Harry did anything. As long as it didn’t affect the company. That was all that Norman Osborn cared about. He didn’t even know that his son was filing to be emancipated or had legally changed his last name to Lyman not that long ago. He was trying to get his father to notice him but he would have to jump off a building to do that it seemed. 

“You finally decided to come home,” Norman said as he entered.

“Peter was missing so I went to help find him,” Harry said.

“This isn’t affecting your grades?” Norman asked.

“I thought you liked Peter?” Harry asked him.

“I don’t think you should date someone who has a habit of cheating and using people,” Norman said. Harry looked surprised that his father was accusing his boyfriend.

“Why does that matter to you?” Harry asked. “I can take care of myself without you forcing me into a marriage.” Norman seemed surprised at the accusation. Harry didn’t know why he was surprised. He had decided that marrying his son to his best friend was better than having his son just date whoever he pleased.

“I know I was acting rash with that decision and I apologize,” Norman said. “I got some paperwork today that I signed. I figured you would want to know. I don’t know why you want to be seen as an adult Harold, but I would suggest you think twice before throwing it all away.”

“I just was thinking of my future,” Harry said. Norman seemed to think about that before he left his son. Harry was confused. Norman never pushed him off for something else. Something had to be gone on and Harry wanted to get to the bottom of it sooner rather than later. He rather knew what his father was up to then finding out when whatever had been decided was decided. 

~

Peter was in the lab alone. He rarely had an opportunity like this. He would have gone in and worked on his other three projects but Peter had a focus. Something he needed to do. He worked on it and made sure no one bugged him as he continued in the lab. Harley and Harry had come in and checked on him occasionally but he kept his project from them. Pepper even tried to see what he was doing but he wasn’t ready for her to know what he was working on. She would probably make him stop. 

Peter made it his goal to see Tony once a day and tell him what he was working on. He knew his father would be mad but right now he only cared about protecting his family.

“I even add an AI like FRIDAY and JARVIS,” Peter told his father. “I call her KAREN though. Kinda like that nanny I had when I was ten who would play that crappy music and make fun of me in French as if I didn’t know how to speak French.” Peter realized that he wasn’t going to get a response from his father.

“I choose red and blue. Our colors. I wish that you were awake to help me with this. I know you wouldn’t approve but I have to protect them. I have to stop him before he attacks and hurts anyone else,” Peter said. Tony laid there and Peter listened for any sign of change in his heartbeat but there wasn’t one. Peter sighed before going back to the lab and back to his project.

~

Pepper was concerned about what was happening with her son. She had seen him in the lab but he was being like Tony when Tony got back from overseas. She wondered somedays if she should expect an Iron Man suit to show up on the news or if she should be asking FRIDAY about what he was doing. She knew Peter needed space after whatever happened but this was getting out of hand. Something had happened and no one was telling her the complete truth. She was going to have to find out through the record in the lab but FRIDAY had so far reported nothing. 

“Why are you so worried?” Rhodey asked. “He isn’t Tony’s birth son. He isn’t exactly like the man.”

“That is where you are wrong. Peter is exactly like Tony because he watched Tony growing up and believed he was his father for most of his life. Peter is a Stark because he was raised as a Stark and nothing we say will change that,” Pepper said. 

“He isn’t building a suit in the lab. Tony has a protocol for that,” Rhodey said.

“This is Peter though. What if he beats that protocol or he is working on making something that is like the suits?” Pepper asked.

“Peter wouldn’t do that. He might want revenge but he isn’t going to seek it. He never has,” Rhodey said. 

“I don’t think it is the same as when he was a kid. Something happened when he was with Richard,” Pepper said. Rhodey saw the concern as Pepper left him to go check on her daughter. Peter was up to something and no one would be able to figure out.

~

Peter got into the suit on the roof and stood on the edge before he jumped. He felt the air rush past him as he held up his arm and then swung towards another building over the city. Peter grinned as he did a flip and landed on a building. He had succeeded at creating the next Iron Man, Spider-Man. 


	3. Spider-Man

**Summary for the Chapter:**

> Peter becomes Spider-Man. Harley and Harry are worried about him. Pepper finds out about Tony being Peter's dad.

Peter didn’t mean to make this a serious gig. Climbing on walls. Swinging through the city. Stopping common criminals. It was a little small for a Stark but he was not just a Stark. He was everyone who made him who he was. He decided that saving lives while waiting for another Goblin attack was the best option. Besides fighting, small-time criminals were great practice for when the Goblin showed up. He didn’t know how to tell his boyfriends though. 

“Where were you?” Harley asked when Peter was heading to his room. He was trying to hide a bruise that was on his skin. 

“I need some fresh air,” Peter lied, heading for his room. Harley stopped him and turned him to face him. Peter let a gasp. He was surprised. Harley touched Peter’s cheek which was where his bruise was at.

“What happens?” Harley asked.

“Some guy thought he was better than me,” Peter said. Harley kissed his cheek as he looked at Peter. 

“Harry will be here soon. How about we cuddle and you can tell us about that big bad man,” Harley said.

“I would like that but I need to spend time in the lab,” Peter said apologetically. He didn’t want Harley to see the other bruises. Harley watched his boyfriend walk away knowing he was hiding something.

~

Harley figured he would tell Harry about what was going on. Harry was dealing with a lot but Harry should know. He should know the truth about their boyfriend. Harry came in looking tired as he laid on the bed watching Harley work at his desk.

“What upset you?” Harry asked.

“Peter has me worried,” Harley said. Harry seemed concerned. 

“He is safe here with us,” Harry told Harley. 

“He came home bruised today,” Harley said. “I confronted him but he just changed the topic as if it was not my place to know about it.” 

“That’s not good,” Harry said, feeling worried about their other boyfriend. “Maybe I could talk to him?”

“He’s in the labs,” Harley said. Harry nodded before going down to Peter’s lab which was empty. It was neat and organized as if Peter hadn’t been down there for a couple of days. Harry went up and knocked on Peter’s door. No one said anything so he went in to hear the water running. He texted Harley asking him to meet him in Peter’s room. Harry sat on Peter’s bed waiting for his boyfriend. Harley came in and joined Harry while waiting. Peter came out in nothing but a towel. Harley and Harry watched the look of surprise before their eyes reached the bruises. Peter looked down hoping that they wouldn’t worry too much. Harry and Harley were surrounding Peter in seconds. 

“What happened?” Harley asked as Harry looked over for each bruise. Peter was blushing as the two boys looked over him protectively. 

“I told you I got in a fight,” Peter muttered before both boys pulled him into a hug. Peter didn’t expect them to pick him up and help him get ready for bed. Peter was pulled between them so they could cuddle and hold him. Harley and Harry had made sure to kiss each bruise. They made sure that he was alright as they all fell asleep. Peter watched them fall asleep before he allowed himself to sleep knowing they were safe before he could close his eyes. 

~

Pepper was raising two children on her own. Her teenage son was dealing with something that she didn’t know about. She knew the files came in and she had looked over them but she hadn’t found anything yet. She opened up one of Peter’s private files and stopped. It was a paternity test for Richard and Peter. It came out as Pepper knew it would. She looked at the next file and froze. It was a test against Peter and Tony’s DNA. She didn’t expect the result. She didn’t expect to see the result. 

“FRIDAY, where is Peter?” Pepper asked.

“He is in his room asleep with Mr. Keener and Mr. Osborn,” FRIDAY said. Pepper figured that he would need to talk but her son needed sleep. Besides she had another child to check on now. Pepper found her daughter asleep as she watched one of her children. She knew they both were safe, but something had her worried.

~

Pepper was in the room with her husband. She had come to check on him and make sure he was okay and that he may wake up.

“I don’t know what to do anymore,” Pepper told him. “Our son is up to something. He is hiding in the labs and coming home late. I know he is lying to Harley and Harry. I know he is yours but that changes nothing. I just want him to come back to us but he is inside his head like you were after Afganistan. I’m worried he might try to avenge you.”

Tony just laid there and he didn’t say anything. Pepper felt a tear fall as she kissed his cheek. He would wake eventually. Helen had said so but now he had a son who was risking his life somehow and no one knew what was going on with him. She looked at Tony one more time before she went back to look over the files that Peter had been working on hoping for some answers. 

~

Peter had woken up surrounded by Harry and Harley. He smiled as he closed his eyes hoping they would think he was asleep if they woke up. It felt comfortable being there and knowing those two cared about them. He felt Harley move as he kissed Peter’s forehead before he felt him move over him. He figured he was kissing Harry’s forehead as well. Harley got up leaving Peter cold. He shivered as Harley chuckled and whispered something about coming back. He moved closer to Harry as Harley was gone. He felt Harley get back in bed a while later as he was chuckling. 

“Cold love,” he muttered. Peter nodded proving that he was in fact awake. “Did I wake you?”

“No,” Peter said.

“Can you two not have morning pillow talk until I’m awake?” Harry groaned. Harley and Peter smiled at him before Harley turned his focus back on Peter. His hand touching where the bruises were the night before. 

“They are gone,” Harley whispered. Peter nodded. He was barely holding it together with hands-on his chest. He looked at Harley and saw the blond smiling at him. 

“I heal fast,” Peter said. He didn’t know the extent of the healing power but he knew it worked pretty fast. Harley nodded as he kissed the other boy’s neck. Peter let out a small gasp which got him a smack by the boy next to him that was trying to sleep. Harley couldn’t help it as he started laughing which caused Harry to groan. 

“Can I get any sleep?” Harry asked.

“What were you doing before we woke you up?” Harley asked him. Harry grumbled as Peter smiled at the other boy. Harry saw the smile on Peter’s face and was just glad to have his boyfriend happy. It had been a while since he saw Peter genuinely smile. 

“What are the plans for the day?” Harry asked.

“Mini-Boss has a meeting with Mrs. Boss this morning,” Friday replied. Peter was surprised by that. He was just planning to work in the lab. 

“When do I need to meet her?” Peter asked.

“She has made breakfast for you and her this morning and would like you to meet her in Conference Room C,” FRIDAY said. Peter still surprisingly kissed his two loves on the forehead before he went off to find out what was going on.

~

Peter came into the room to see his favorite breakfast foods. He looked surprised as Pepper drank her coffee and read the paper. Something he became used to while growing up being raised by the woman. This wasn’t something that his mother normally did. Something was up. 

“Did I do something wrong?” Peter asked his mother. 

“Sit down and eat something,” Pepper said as she smiled at her son. Peter did as he was told. He watched his mother waiting for the shoe to drop and her saying something about spider-man. The same spider-man who was on the cover of the newspaper she was holding. 

“Why the special breakfast?” Peter asked. Pepper put down the paper and smiled.

“Your dad and I were talking before all this happened about you looking at colleges for the coming year. He was thinking MIT, but I was thinking something closer to home,” Pepper said. 

“You just want to talk about colleges?” Peter asked.

“I figured that would be a better topic than starting off with why you went to Malibu,” Pepper said looking at her son.

“I wanted to visit Mary,” Peter said. Pepper didn’t expect that. “I just found out that the biggest lie of my life wasn’t a lie and I just wanted to yell at her.” 

“Your dad and I were worried when we couldn’t find you,” Pepper said. 

“I should have told you both what I was doing,” Peter said. Pepper saw him look defeated. She moved over to him and pulled him out of his chair so she could hug her son. Peter seemed surprised but he hugged her back as he cried into her shoulder. 

“I’m sorry, Mom,” Peter said.

“I should have told you that Richard wasn’t your father, but I didn’t know who your father was and I didn’t want you to think that I might,” Pepper said. Peter seemed surprised.

“You knew,” Peter said. 

“I did,” Pepper told him before she looked him in the eyes. “Mary told me when she found out she was pregnant. She said you weren’t Richard’s but never mentioned your father by name.”

“Oh,” Peter said. “I guess she worked for Dad and that they were dating.” Pepper nodded waiting to see what else Peter would tell her. He said nothing else as she saw the tears falling. 

“I should have brought it up when all of this came out. Maybe we would have found the truth sooner rather than later,” Pepper said. Peter nodded as Pepper saw her son over for any injuries. He seemed fine. 

“Thanks for raising me,” Peter said. Pepper seemed surprised. 

“That’s what a parent is for,” Pepper said. Peter let her hug him again as she held her son close. Her boy, not Mary’s. She had raised him as her son. Tony may have been present but this was her little boy. The same boy she would hold when he was little and couldn’t sleep or bandaged up when he was hurt on the playground. She didn’t want to let her boy go as he held on to her but she knew he was about to start college. He was about to do great things and she couldn’t stop that. Pepper would have to watch her son leave the nest soon. 

~

Peter had an amazing morning with his mother, but he needed to find Goblin. His luck came out bad again when Goblin didn’t show up. Peter swung back to the tower and crawled in his window. He made sure his door was closed before he took off the mask. He was about to hit the emblem on his suit when he felt two presences in the room. He turned to his bed to see Harley and Harry looking surprised.

“What the fuck?” 


	4. With Great Power Comes Great Responsibility

Peter looked between his boyfriends. They both looked him over as he touched the spider-emblem. He got out of the suit as he went to grab at least a shirt. Once he was in clothes and the suit was put up he waited. Harry was the first to break.

“How long has this been going on?” he asked. 

“Since the incident,” Peter said. Harley and Harry looked at each other. 

“Why didn’t you say something?” Harley asked. Peter looked at his feet.

“I didn’t want you both to be in the place where you would have to try and deny something to my mom,” Peter said.

“Peter, we would keep your secret no matter the cost,” Harry said. Harley agreed. Peter looked up as he saw two bodies pulling him into a hug. Peter let them hold him for a bit. He didn’t deserve them. He rested his head on Harley’s shoulder as he felt them hold on to him. He felt safe for the first time since watching his dad get hurt. 

~

Pepper was asleep next to Tony when she heard something. She woke to see a doctor looking surprised. Tony was mumbling. 

“Tony?” Pepper asked. Tony opened his eyes and looked at his wife. He smiled. 

“Hey Pep,” he said. He looked at the room before something set in. “where’s Peter?”

“He’s probably asleep,” Pepper said.

“He is currently in his room with Keener and the better Osborn,” FRIDAY said. 

“FRIDAY is a dear and gets my son down here,” Tony said. Pepper looked concerned.

“Peter is fine,” Pepper said.

“I need to talk to my son now,” Tony said. She knew Tony knew as well. She looked at him and let him do what he wanted. Starks is stubborn. She had raised two of them and practically had to keep another one from getting in trouble all the time. She didn’t want to fight Tony when what he wanted was to speak to his only son. Her son.

~

Peter was in MedBay the second he got the message from FRIDAY. He ran to his dad when he saw him talking with Pepper and hugged him. Peter felt the tears as his dad put his arms around him. 

“It’s alright,” Tony said. “I’m fine, Bambino.”

“I just thought I lost you for good,” Peter said. Tony smiled at his son as Pepper left them to give them some space that they needed.

“I’m here,” Tony said making sure his son was alright. He saw a small bruise on his arm but Peter seemed alright for the most part. He looked at his son who looked tired. As if he was trying to hold the world on his shoulder again. It was such a Peter thing to do. 

“I’m sorry, Papa,” Peter said.

“How are you?” Tony asked his boy.

“I’m fine. I just feel like I should have helped then,” Peter said. 

“There is nothing you could have done,” Tony said.

“There is though. I could have helped,” Peter said. 

“No, you couldn’t,” Tony said.

“I have these powers and if I don’t use them then someone will get hurt again,” Peter said. “It could be anyone I care about and I can’t let that happen.” Tony looked at his son worriedly. Pepper came in to bring Tony some water and food before she left them to talk. Tony looked at his son waiting for him to say it.

“Peter, you didn’t think about recreating the suit,” Tony said. 

“I didn’t recreate the Iron Man suit,” Peter said. Tony looked at his son and knew he wasn’t lying, but he also knew he was hiding something. Peter had done something. 

“What did you make something equivalent to an Iron Man suit?” Tony asked him. 

“Not exactly,” Peter said. 

“Peter James Stark,” Tony said. “Tell me you haven’t been going after this Goblin man.”

“I may have been waiting for him to show up,” Peter said. Tony grabbed his head wanting to complain about his son’s recklessness.

“I didn’t want you following my career path for a reason. Being a hero causes trouble,” Tony said.

“I know that but if I can help with small crime,” Peter said.

“How long?” Tony asked.

“A while now,” Peter said. Tony looked upset. 

“What if you got hurt?” Tony asked.

“I wouldn’t,” Peter said. Tony looked at the bruise on his son’s arm. Peter noticed. “It will heal before tomorrow. They all heal before the next day just ask Harley and Harry.”

“I’m not going to be able to stop this am I?” Tony asked. He wanted to ask how Harley and Harry knew but he figured that was a conversation for another time. 

“No,” Peter told him. Tony looked at his son. He was the spitting image of him.

“So have you told anyone about what you told me?” Tony asked.

“Mom found out when she was looking over files but besides that no,” Peter said. Tony looked at his son and smiled. 

“We can tell them later. How has everything been going?” Tony asked.

“Besides me now being a vigilante? I aced a few tests and been spending most of my time in the labs,” Peter said. 

“I don’t approve of it but as long as you are doing it ongoing to make some adjustments to whatever idea of a suit you have,” Tony said. Peter knew he would get no other deal from his father. 

“I missed you,” Peter said. Tony smiled at his boy.

“I missed you two, Kid,” Tony said. Peter hugged his dad again not wanting to let go and loss him to something else. He couldn’t lose him again. 

~

Peter was swinging through the city when he heard the glider. He followed as the Goblin attacked Stark Tower again. Peter wanted to scream at the idiot as he went and hit him with a web.

“Oh so the web-head is a fan of the Stark family as well,” Goblin said. 

“I’m loyal to the Avengers,” Peter said as he tried to hit Goblin with another web. Goblin moved out of the way as he laughed. Peter growled annoyed with the man who had hurt his father. The man who had tried to take the one thing he cared about more than anything.

“The Starks are nothing but liars,” Goblin said throwing a pumpkin bomb that Peter dodged trying to find a way to keep from getting hurt. He needed to stop Goblin now. While he had the chance. He was right here. He was able to stop the man once and for all. He could stop him and then protect his family. He could save them. This Goblin had a grudge against the Stark family for some reason and whatever reason that was, he would find it and stop this man.

“You know nothing about the Starks,” Peter hissed as he missed another bomb. Rhodey appeared and the Goblin saw his new target but Peter made him turn his focus back to him. 

“Why do you care so much for them?” Goblin asked. “You protect them yet they stay inside and hide or you shoo them away like flies.”

“My dad taught me three things when I was younger,” Peter said as he missed another bomb and made sure Rhodey stayed back from the fight. The other hero seemed uncertain but he stayed back as he got on comms with the other avengers.

“One, never let your enemies see your fear,” Peter said having KAREN access ways on how to take down Goblin. She called out a way and Peter smiled. “Two, always know your enemies’ weakness.” Peter hit Goblin’s glider and swung it into the building as he went for Goblin and held him to the building.

“What is the last thing?” Goblin asked. He seemed to be figuring out a plan.

“Starks are made of Iron,” Peter said. As he lowered the Goblin and him down before webbing up the villain. He took off the mask and his breath caught. The other avengers came as they helped to cart off Norman Osborn. Peter watched as Harry came out and screamed at his father as Harley held the other boy back. Peter felt his knees weakening as Rhodey landed next to him. His head was pounding as he looked at the older hero who was trying to say something. Rhodey realized something was wrong.

“Focus on me and breath,” he could make out after a while. He did so as he finally got air in his lungs. He looked at Rhodey who saw the boy calm finally.

“You okay?” Rhodey asked.

“Yes,” Peter said. “I-I just need to get home.”

“You sure? You just had a panic attack,” Rhodey said.

“My dad is in the hospital and I need to make sure he is okay. Now that Goblin is taken care of,” Peter said. Rhodey shocked his head. 

“You need to get to MedBay so we can make sure you have no injuries,” Rhodey said. 

“I’m fine but someone should make sure Harry is alright. He just found out his dad has been terrorizing people,” Peter said before Rhodey could say something else. Peter webbed himself away and entered into his room before getting out of the suit. He got in some clothes before heading down to MedBay. His dad was perfectly fine as he entered. He sat down next to him as he watched him sleep. Rhodey came in with Harley and Harry after a bit who found Peter asleep next to his father. 

“You guys should take him back to his room. When Tony wakes up he will want to know that Goblin attacked again and Peter doesn’t need to hear about that,” Rhodey said as the other two picked up Peter. Rhodey watched them leave as Tony opened his eyes. 

“You doing alright?” Rhodey asked.

“Was Peter just here?” Tony asked.

“I had Harley and Harry care him off to bed,” Rhodey said. 

“He was saying something about not worry about the Goblin anymore,” Tony said.

“Spider-Man took care of the Goblin,” Rhodey said. “Definitely, Avenger material in that kid, but I would give it a few years.”

“So that is what he is calling himself,” Tony said with a snort. Rhodey was confused. 

“What are you talking about?” Rhodey asked.

“Spider-Man is most likely my son. Let me guess he appeared a few days after my incident in some high tech suit that looks like it came from some tech company,” Tony said.

“Yes,” Rhodey said.

“He went after the Goblin the second he arrived?” Tony asked.

“Yes,” Rhodey replied again.

“Peter admitted to making a suit but didn’t say what it was. Whatever Richard did to him affected him,” Tony said as his friend looked at him in disbelief. Pepper came in and saw Rhodey’s face and looked at Tony.

“Did I miss something?” She asked.

“Just our son parading around New York as a new Spider vigilante,” Tony said as he turned on the TV that was reporting the fight from the day. Tony paused as he saw who the Goblin was. 

“Harry didn’t take that too well. He was cursing his father as they dragged him away,” Rhodey said. Pepper was more focused on her son who was in the video in a suit.

“I can’t believe he would do something like that,” She said. 

“He is my son,” Tony said as Rhodey and Pepper watched the news report. “I’m surprised that Norman did something like that. It seems below him in away.”

“Maybe he found out somethings about the boys?” Pepper suggested. Tony felt his blood run cold. If he found out anything about his son then Peter was in trouble except then he realized that the main things he probably found out were about Peter not being his son which was false. 

“Norman Osborn is a fool,” Rhodey said.

“Not as much as we are. Rhodey there is something I have to tell you,” Tony said. Rhodey looked at his friend confused.

“Yes?” Rhodey asked.

“Peter is my son.”


	5. At the End of the Day

Rhodey was shocked, to say the least. Tony had always said there was no way that Peter was his only to turn around and tell him that Peter was his. 

“You said he wasn’t,” Rhodey said. 

“He is,” Pepper said. “We didn’t know until now.” 

“How did you find out?” Rhodey asked. Tony smiled at his friend.

“My son decided to run some DNA test and then go missing for a bit,” Tony said. 

“Sounds like a Stark,” Rhodey said. 

“It does,” Pepper said. “Peter is exactly like his father.” Tony looked offended for a bit. He then smiled thinking about his son. His boy, who had just protected his family. Tony looked at his friend and wife and smiled.

“I think I need to be getting up to check on my son,” Tony said as he went to get up but Pepper and Rhodey held him down. 

“Peter is asleep anyways. You need to rest as well,” Pepper said. Tony agreed though he rather not be in MedBay for another night, dealing with Pepper’s wrath from not listening was worse.

~

Peter start drift awake between Harley and Harry. The two boys were comfortable. He felt lips on his forehead as Harry whispered something to Harley. Harley said something back but Peter was still in between wake and sleep. Peter opened his eyes as the two went quiet. Harry smiled at him as he kissed his cheek. He felt Harley kissing the other one as he closed his eyes and wanted to just drift again but he knew he needed to get up. He opened his eyes as Harry ran his fingers through his hair as he felt Harley’s lips kissing his jawline. Peter groaned as the two boys smiled.

“I just want sleep and cuddles,” Peter said. 

“Come on baby boy,” Harry said. Harley laughed at something and Peter heard a smack and Harley saying ouch. Peter opened his eyes to see Harley holding his arm which must have been smacked. Harry was grinning at Peter.

“Why must you wake me up in the morning?” Peter asked. Harley and Harry smiled as they both kissed his cheek again. Peter looked at them both confused.

“Your dad is getting released today,” Harley finally said. “Pepper told us to tell you when you were more awake and we figured that was cause for celebration,” Peter remembered what they didn’t know. 

“You know we never talked about when I left for that week,” Peter said. The two froze having all but forgot with everything else going on. They looked at each other before looking at Peter.

“You don’t have to tell us if you are not ready,” Harley said. 

“I want to tell both of you,” Peter said. Peter looked at them smiling knowing he wanted to tell them everything. “I did a few DNA tests just to see who my dad really was. Richard Parker wasn’t my father.”

“Then who is?” Harry asked. Peter started laughing at the question which shocked the two boys.

“I’m sorry but it’s funny because my actual dad is Tony Stark and I just realized how all of this was started because I thought I was adopted,” Peter said. The two looked surprised before they both thought about it.

“Well you are a mini Tony,” Harry said.

“Don’t say that too loud,” Peter said. 

“Why not?” Harley asked. Peter look at them like they were joking.

“He may hear you and get excited about that,” Peter said. Harley and Harry realized for the first time that Tony knew and was happy about this. Peter was Tony’s son through and through and this cemented the fact that he was his son. 

“How did he take it?” Harry asked.

“Really well for someone who didn’t care for most of my life,” Peter said.

“Oh so that is what you tell your friends,” Tony said. Peter, Harley, and Harry looked surprised as the older man looked a little hurt by the comment. 

“Hi Dad,” Peter said but Tony just left. Peter got up to get dressed so he could go after his father and talk things out. Harley and Harry both watched as the other boy left after his father.

~

Peter and Tony had a spot that was where one of them went if they were upset. Peter found his father there working on something.

“I feel bad for saying it,” Peter told his father. Tony looked at the boy before turning back to his project.

“In your defense, I wasn’t around much,” Tony said. 

“I’m sure you had some reason for not being there for part of my life,” Peter said. 

“No, I didn’t,” Tony said turning to his son. “You have a right to hate me for pushing you away as if you are some mistake. I only took you in for PR reasons but I didn’t think I would become attached to you. Pepper may have raised you but I wanted to help. I just didn’t want you to turn into me so I stayed back. I figured being away would be better than turning into Howard.” Peter looked surprised.

“You are not him,” Peter said. “You cared enough to keep me in a grade level with my peers and to make sure I was taken care of. I remember you talking with Pepper about me when I was little. Then I wondered why you couldn’t ask but now you saying that just shows you cared but you were scared of what it would do to me if you acted as you cared.” Tony was surprised as his son wrapped his arms around him and thanked him for being there for him. Tony didn’t know how to react so he hugged him back and asked if Peter wanted lunch figuring they both should leave the lab and find a better coping space.

~

Happy was in shock as they explained how Peter was actually Tony’s son. Peter smiled as the man looked between them all.

“So you are telling me that Peter has always been Tony’s?” Happy said. 

“Yes,” Pepper said. 

“Then why was I told differently,” Happy said grumpily as always. 

“We didn’t know until recently,” Tony said. Happy looked annoyed but left it at that as he left them to go out and do something that was non-Stark related. 

“I think we should celebrate,” Peter said. The family all turned surprised. It was a mix of Avengers and Stark family or like family. Tony smiled at his son.

“What are we even celebrating?” Nat asked.

“Everyone is home, the lives we lost a new hero on the streets. Take your pick.” Tony said. 

“I say we can celebrate to some fresh starts thanks to Spider-Man arresting the Goblin,” Harry said with a smile.

“How about everyone in this room right now?” Pepper said. The team nodded as they cheered that they were all there. Peter smiled as he felt two sets of arms pull him to the couch as he laughed. He was happy for the first time in a while. He didn’t worry about stepping up to his father’s shadow and he didn’t feel abandon. 

~

Peter wanted to fight Harry on the idea and Harley was with him. Harry had suggested moving in together but Harry didn’t say he already bought a place for them to live in. 

“No,” Peter said. “I can pay for myself and Harley is capable of using his allowance to pay for himself.”

“But that’s the thing. I wanted to do something nice for the both of you,” Harry said. Harley looked ready to complain again about it when Peter held up his hand. 

“Maybe we can compromise since you bought the place, we take care of the furniture and anything else like food and necessities,” Peter said. Harley seemed to like that idea as he looked at Harry. 

“Done,” Harry said. The boys all smiled at each other as Peter and Harley went to announce the move to Tony. Peter was worried about what his father would say but Harley held his hand as they had to the tower. 

~

“You want to move in with Harry?” Tony asked again for the fifth time as Pepper held back a laugh. They had been talking about this for two hours and Tony had repeated that question a few times now. 

“Dad, it’s not like I’m moving out of state and it would make sense for when I’m going to Columbia,” Peter reminded his father.

“Why not MIT?” Tony asked.

“Because you went there and I don’t want to be far from home,” Peter said. “I actually can stand you as my father.” 

“Well then I expect dinner once a week if you move out,” Tony said. 

“Relax old man,” Harley said. “I will be there to keep Peter in line.”

“Harry and Harley will be at these dinners and you three will be giving me updates about what is going on in your lives,” Tony said. 

“I can give you some details right now,” Harley said. Peter put his hand over Harley’s mouth who looked shocked. 

“My dad doesn’t need to hear about that,” Peter said. Harley licked Peter’s hand which surprised the boy as he moved his hand away.

“I do not need to hear about those details. I would also prefer to think my son is asexual so please never mention that again,” Tony said giving Harley death stares. Harley just smirked as Peter groaned about how annoying his boyfriend was. 

“So you are okay with me moving in with two boys?” Peter asked.

“I’m fine with it as long as you are happy,” Tony said looking at his son. Peter smiled as he went to begin packing. Tony stopped Harley. “You or Harry hurt my son and I have a few assassins who would love to take out a few boys for Peter Stark.” Harley nodded before running after Peter to get away from Tony. Tony just smiled knowing he got his message across.

~

“Cheers,” Peter, Harley, and Harry said as they sat on their new couch in their living room. Peter had suggested the celebration as the three of them rested from all the unpacking. Harry was between Harley and Peter as they talked about plans for their new place. Peter talked about some stuff they could get and dropped the word dog in every once in a while. Harley and Harry now had an idea for Christmas which was still a few months out. Harley had been talking about the meals he could make since the other two couldn’t cook. Harry just listened as they both talked and threw in his two scents ever once in a while. The three enjoyed this moment where it was just the three of them alone. They hadn’t had a moment like this since they all got together always at Peter’s place where there was bound to be someone. 

“I’m thinking of a bath to relax,” Peter said. Harley and Harry both agreed. 

“You know this is the first time we are all on our own,” Harley pointed out.

“But we aren’t alone,” Harry said as he looked at the other two. “As long as we have the three of us, none of us will be alone.” Peter agreed as he kissed both of their foreheads before heading to start the water.

“Don’t think about undressing before we get in there, Stark,” Harley said. Peter just rolled his eyes as he thought about how different his life was. He knew that they still had bumps ahead but that they would be alright. Besides Spider-Man was there to protect them now.

**Notes for the Chapter:**

> This is the ending. I may come back later and do some one-shots but for now, this is all. If You like ph^2 as much as I do check out other works by all the amazing writers who write for this tag!


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